This preliminary report details the results of looking for pathway enrichment in each of the groups of genes produced by hierarchical clustering of the drug perturbations. I’ve cut the the data into 15, but this value can be changed if we decide on a different value. Otherwise, this analysis focuses on enriched pathways in the KEGG database. Specifically, this analysis uses the C2 KEGG segment from: https://www.gsea-msigdb.org/gsea/msigdb.

As for this report, the panel on the left is sorted by the number of dark kinases in the cluster and displays both the number of pathway hits and dark kinases in the cluster. The number of each cluster is arbitrary. The entry for each cluster displays the kinases associated with the cluster along with the number of non-kinases genes. Below this table are the pathways that passed the enrichment analysis at the 0.01 false discovery rate level. I also corrected for running this analysis for all 15 clusters.

Overall Enrichment Stats

Overall, 103 pathways are enriched in at least one of the following clusters. Of these pathways 60 are only hit once. The following pathways are seen in two or more clusters:

Num: 4 (Pathways: 18 DK: 27)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (27) CAMKK1, CDK11A, CDK12, CDK17, CDKL1, CLK3, COQ8A, CSNK1G1, CSNK2A2, DYRK2, HIPK1, MAST2, NEK1, NEK4, NEK7, PAN3, PDIK1L, PHKG2, PIP5K1A, RIOK3, SCYL1, STK19, TAOK1, TESK1, TLK1, TLK2, ULK4
Light Kinase (61) ABL2, ADPGK, ARAF, ATM, AURKB, BAZ1A, BAZ1B, BRD4, BTK, BUB1, CAMK2A, CAMK2G, CDK1, CDK2, CDK3, CHEK1, CLK1, CSK, DDR2, DGKE, DGKZ, FER, GRK2, GRK7, GSK3A, GTF2F1, HKDC1, HSPB8, IRAK3, LYN, MAP2K7, MAP3K6, MAP4K4, MAPK6, MAPK7, MAPK8, MASTL, MELK, MLKL, MYLK2, NEK2, PAK1, PAK2, PASK, PI4KB, PIK3C3, PLK4, RPS6KA5, SIK1, SIK1B, SLK, SMG1, SRPK1, STK10, STK35, STK4, TPTEP2-CSNK1E, TTN, TYRO3, WEE1, YES1
Non-kinase Count 2741
label pval fdr signature geneset overlap hits
KEGG_SPLICEOSOME 0.0e+00 0.0e+00 2829 127 51 ACIN1,ALYREF,BCAS2,CDC40,CHERP,CRNKL1,DDX23,DDX46,HNRNPA1,HNRNPA1L2,HNRNPA3,HNRNPK,HNRNPM,HNRNPU,HSPA6,HSPA8,ISY1,LSM8,MAGOHB,PHF5A,PQBP1,PRPF18,PRPF38A,PRPF6,PRPF8,PUF60,RBM17,RBM22,RBM25,RBM8A,RBMX,SART1,SF3A2,SF3A3,SF3B2,SLU7,SNRPA,SNRPA1,SNRPB,SNW1,SRSF2,SRSF4,SRSF6,SYF2,TCERG1,THOC1,THOC2,TRA2B,U2SURP,WBP11,XAB2
KEGG_CELL_CYCLE 0.0e+00 0.0e+00 2829 124 38 ATM,BUB1,CCNA2,CCNB1,CCNB2,CCNE2,CDC16,CDC25A,CDC25C,CDC27,CDC6,CDK1,CDK2,CHEK1,CREBBP,CUL1,E2F1,E2F2,E2F3,ESPL1,HDAC1,MCM3,MCM4,MCM7,MDM2,ORC6,PCNA,RAD21,RB1,RBL1,SFN,SMAD4,SMC1B,SMC3,STAG1,STAG2,TFDP2,WEE1
KEGG_PROTEASOME 0.0e+00 0.0e+00 2829 46 21 POMP,PSMA1,PSMA2,PSMA3,PSMA7,PSMB2,PSMB5,PSMB6,PSMB7,PSMC1,PSMC2,PSMC3,PSMC4,PSMC6,PSMD1,PSMD12,PSMD2,PSMD6,PSMD8,PSME2,SEM1
KEGG_RNA_DEGRADATION 0.0e+00 0.0e+00 2829 59 22 C1D,CNOT10,CNOT2,CNOT3,CNOT4,CNOT6,CNOT6L,CNOT9,DCP1A,DCP2,DDX6,DIS3,EDC4,EXOSC10,EXOSC3,EXOSC4,EXOSC5,EXOSC9,HSPA9,LSM8,PAPOLA,TENT4A
KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS 0.0e+00 0.0e+00 2829 134 32 CDC16,CDC27,COP1,CUL1,CUL3,CUL4A,CUL5,DDB1,ERCC8,FBXO2,FBXW11,FBXW7,ITCH,MDM2,PIAS2,PML,RCHY1,RNF7,SMURF1,TRIP12,UBA2,UBA6,UBE2A,UBE2C,UBE2D3,UBE2I,UBE2K,UBE2M,UBE2Z,UBE3A,WWP1,XIAP
KEGG_OOCYTE_MEIOSIS 0.0e+00 0.0e+00 2829 112 28 BUB1,CAMK2A,CAMK2G,CCNB1,CCNB2,CCNE2,CDC16,CDC25C,CDC27,CDK1,CDK2,CPEB1,CUL1,ESPL1,FBXW11,ITPR3,PPP2CB,PPP2R1B,PPP2R5C,PPP2R5D,PPP2R5E,PPP3CC,PPP3R1,SLK,SMC1B,SMC3,SPDYA,STAG3
KEGG_ENDOCYTOSIS 0.0e+00 9.0e-07 2829 181 31 ACAP2,AP2B1,ASAP1,CHMP4B,CHMP5,CLTA,CLTB,CLTC,DNM1L,DNM2,GRK2,GRK7,HGS,HSPA6,HSPA8,ITCH,MDM2,PARD3,PIP5K1A,RAB11FIP2,RAB5C,RBSN,SH3KBP1,SMURF1,STAM,USP8,VPS37A,VPS45,VPS4A,VPS4B,WWP1
KEGG_HUNTINGTONS_DISEASE 1.0e-07 2.5e-06 2829 180 30 AP2B1,ATP5F1B,ATP5PB,CASP3,CLTA,CLTB,CLTC,COX5A,CREB1,CREBBP,CYC1,DCTN4,HDAC1,HTT,NDUFA10,NDUFA9,NDUFS3,NDUFS7,NDUFS8,NRF1,POLR2A,POLR2J2,SLC25A5,SOD1,TBPL2,UQCRC2,UQCRH,VDAC1,VDAC2,VDAC3
KEGG_HOMOLOGOUS_RECOMBINATION 2.0e-07 3.4e-06 2829 28 11 BRCA2,MUS81,POLD3,RAD51,RAD51D,RAD52,RAD54L,RPA2,RPA4,SEM1,TOP3A
KEGG_DNA_REPLICATION 3.0e-06 5.6e-05 2829 36 11 MCM3,MCM4,MCM7,PCNA,POLD3,POLE,RFC1,RNASEH2A,RNASEH2B,RPA2,RPA4
KEGG_P53_SIGNALING_PATHWAY 4.8e-06 8.1e-05 2829 68 15 ATM,BID,CASP3,CCNB1,CCNB2,CCNE2,CDK1,CDK2,CHEK1,COP1,MDM2,MDM4,RCHY1,SFN,TP73
KEGG_APOPTOSIS 6.6e-06 1.0e-04 2829 87 17 ATM,BID,CAPN2,CASP10,CASP3,CASP6,CASP7,DFFB,EXOG,IRAK3,NFKB1,PPP3CC,PPP3R1,TNFRSF10A,TNFRSF10D,TRAF2,XIAP
KEGG_PATHWAYS_IN_CANCER 8.8e-06 1.3e-04 2829 325 39 ARAF,AXIN1,BID,BRCA2,CASP3,CCNE2,CDK2,CREBBP,CTBP2,DVL2,DVL3,E2F1,E2F2,E2F3,EGLN2,FGF22,HDAC1,LAMA2,LAMB4,MAPK8,MDM2,MSH2,NFKB1,PIAS2,PLCG1,PML,RAD51,RALBP1,RASSF1,RB1,SMAD4,STK4,TCF7L2,TRAF2,TRAF4,TRAF5,WNT3,WNT9B,XIAP
KEGG_WNT_SIGNALING_PATHWAY 1.3e-05 1.7e-04 2829 150 23 AXIN1,CAMK2A,CAMK2G,CHD8,CREBBP,CSNK2A2,CTBP2,CUL1,DVL2,DVL3,FBXW11,MAPK8,PPP2CB,PPP2R1B,PPP2R5C,PPP2R5D,PPP2R5E,PPP3CC,PPP3R1,SMAD4,TCF7L2,WNT3,WNT9B
KEGG_LYSINE_DEGRADATION 2.5e-05 2.9e-04 2829 44 11 ALDH2,ASH1L,DOT1L,EHMT1,KMT5A,NSD2,NSD3,PLOD3,SETD1A,SETD2,SETDB1
KEGG_NUCLEOTIDE_EXCISION_REPAIR 2.5e-05 2.9e-04 2829 44 11 CUL4A,DDB1,ERCC8,GTF2H1,GTF2H2,PCNA,POLD3,POLE,RFC1,RPA2,RPA4
KEGG_PROTEIN_EXPORT 3.4e-05 3.7e-04 2829 24 8 SEC11A,SEC61A2,SEC62,SEC63,SPCS2,SRP72,SRP9P1,SRPRB
KEGG_NOTCH_SIGNALING_PATHWAY 4.9e-05 5.0e-04 2829 47 11 APH1A,CIR1,CREBBP,CTBP2,DTX3,DVL2,DVL3,HDAC1,NOTCH1,NUMBL,SNW1

Num: 11 (Pathways: 17 DK: 19)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (19) CAMK1D, CAMKV, CDKL3, DYRK1B, LMTK2, LMTK3, MAP3K15, MAPK15, MARK1, MKNK1, NEK5, PIK3C2B, PIP5K1B, SBK1, SCYL2, STK3, TESK2, TSSK1B, VRK3
Light Kinase (46) ACVR1C, ACVR2A, ACVRL1, ANKK1, BMP2K, BMX, CAMK2B, CAMK4, CDK9, CSF1R, DAPK1, DAPK2, DCLK1, EPHA6, EPHB2, EPHB3, FGFR1, FGFR2, FGFR3, FGFR4, FLT4, HCK, ITK, JAK2, KALRN, KSR1, KSR2, MAP2K3, MAP2K6, MAP4K1, MAPK10, MAPK11, MAST1, MATK, PI4KAP2, PRKCG, PRKCZ, PRKD2, PTK2, RPS6KA3, SGK2, SRPK2, STK26, STYK1, TAF1L, TXK
Non-kinase Count 1748
label pval fdr signature geneset overlap hits
KEGG_CELL_ADHESION_MOLECULES_CAMS 0.0e+00 0.0e+00 1813 133 32 CD22,CD34,CD40,CD6,CD86,CDH1,CDH15,CDH2,CDH3,CLDN10,CLDN23,CNTN1,ESAM,HLA-DPB1,ICAM2,ITGA6,ITGAL,ITGAM,ITGB7,JAM3,NCAM1,NECTIN2,NEO1,NFASC,NRXN1,NRXN2,NRXN3,OCLN,SELL,SELPLG,SPN,VCAN
KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION 0.0e+00 0.0e+00 1813 272 42 ADCYAP1R1,ADRA1A,AVPR1A,CHRM4,CHRNA10,CHRNA7,CHRNB2,CHRNB4,DRD2,DRD4,FPR2,GABRA1,GABRA6,GABRB2,GABRD,GABRP,GABRQ,GHR,GLRA3,GRID1,GRIK4,GRIK5,GRIN1,GRM7,HTR2A,LTB4R2,MC2R,NMUR1,NPFFR1,NPFFR2,NPY1R,OPRD1,OPRK1,P2RX7,P2RY1,P2RY8,PTAFR,PTGER4,S1PR3,S1PR5,SSTR2,VIPR2
KEGG_MAPK_SIGNALING_PATHWAY 0.0e+00 0.0e+00 1813 267 35 CACNA1G,CACNA1I,CACNA2D1,CACNA2D2,CACNB2,CACNG7,CHP2,DUSP1,DUSP9,FGF14,FGF18,FGF21,FGFR1,FGFR2,FGFR3,FGFR4,GRB2,IL1R2,JUN,MAP2K3,MAP2K6,MAP4K1,MAPK10,MAPK11,MAPK8IP1,MAPK8IP2,MKNK1,NFATC4,PLA2G2D,PLA2G4A,PLA2G4E,PRKCG,RASGRF1,RPS6KA3,STK3
KEGG_REGULATION_OF_ACTIN_CYTOSKELETON 0.0e+00 2.0e-07 1813 213 28 ACTN2,APC2,CFL2,CHRM4,CYFIP2,ENAH,FGF14,FGF18,FGF21,FGFR1,FGFR2,FGFR3,FGFR4,ITGA6,ITGAL,ITGAM,ITGAX,ITGB7,MYH14,MYL2,NCKAP1L,PIK3R5,PIP4K2A,PIP5K1B,PTK2,SCIN,VAV1,WAS
KEGG_CALCIUM_SIGNALING_PATHWAY 0.0e+00 3.0e-07 1813 177 25 ADCY4,ADRA1A,ATP2A3,ATP2B2,AVPR1A,CACNA1G,CACNA1I,CAMK2B,CAMK4,CD38,CHP2,CHRNA7,GNAL,GRIN1,HTR2A,LTB4R2,NOS1,NOS2,P2RX7,PDE1B,PLCD1,PRKCG,PTAFR,RYR1,RYR3
KEGG_AXON_GUIDANCE 0.0e+00 3.0e-07 1813 129 21 CFL2,CHP2,DCC,DPYSL5,EFNA2,EPHA6,EPHB2,EPHB3,LRRC4C,NCK2,NFATC4,NTN1,PTK2,ROBO1,SEMA4D,SEMA5B,SEMA7A,SLIT1,SLIT3,SRGAP3,UNC5B
KEGG_TIGHT_JUNCTION 3.0e-07 8.6e-06 1813 132 19 ACTN2,CGN,CLDN10,CLDN23,IGSF5,JAM3,MAGI2,MYH14,MYH15,MYL2,OCLN,PARD6G,PPP2R2C,PRKCG,PRKCZ,RAB3B,SPTAN1,SYMPK,TJP1
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 5.0e-07 1.2e-05 1813 265 28 ACVR2A,ACVRL1,CCL26,CCR6,CD40,CD70,CSF1R,CX3CR1,CXCR2,EDA,FLT4,GHR,IFNLR1,IL11,IL12A,IL19,IL1R2,IL23R,IL2RB,IL3RA,IL7,INHBB,INHBC,NGFR,TNFRSF19,TNFRSF8,TNFSF10,TNFSF15
KEGG_O_GLYCAN_BIOSYNTHESIS 8.0e-07 1.6e-05 1813 30 9 B4GALT5,GALNT10,GALNT13,GALNT16,GALNT6,GALNT9,GCNT3,GCNT4,ST3GAL2
KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION 1.0e-06 1.9e-05 1813 116 17 ACTN2,CLDN10,CLDN23,CYBB,ESAM,ITGAL,ITGAM,ITK,JAM3,MAPK11,MYL2,OCLN,PIK3R5,PRKCG,PTK2,TXK,VAV1
KEGG_PATHWAYS_IN_CANCER 3.4e-06 5.8e-05 1813 325 30 APC2,CBL,CDH1,CDKN2A,CEBPA,CSF1R,DAPK1,DAPK2,DCC,FGF14,FGF18,FGF21,FGFR1,FGFR2,FGFR3,FZD9,GLI1,GRB2,ITGA6,JUN,LAMA4,MAPK10,NKX3-1,NOS2,PIK3R5,PRKCG,PTK2,RARB,TCF7,TCF7L1
KEGG_CARDIAC_MUSCLE_CONTRACTION 4.4e-06 6.8e-05 1813 78 13 ATP1A3,ATP1B1,ATP1B2,CACNA2D1,CACNA2D2,CACNB2,CACNG7,COX6B2,COX7B2,MYL2,TNNI3,TNNT2,UQCRHL
KEGG_NATURAL_KILLER_CELL_MEDIATED_CYTOTOXICITY 1.0e-05 1.5e-04 1813 137 17 CHP2,GRB2,ICAM2,ITGAL,KLRC1,KLRC3,NFATC4,PIK3R5,PRKCG,RAET1G,SH2D1A,SHC4,TNFSF10,ULBP1,ULBP2,ULBP3,VAV1
KEGG_HEMATOPOIETIC_CELL_LINEAGE 1.5e-05 2.0e-04 1813 87 13 CD1D,CD22,CD34,CD38,CD3D,CR2,CSF1R,IL11,IL1R2,IL3RA,IL7,ITGA6,ITGAM
KEGG_LONG_TERM_DEPRESSION 4.2e-05 4.8e-04 1813 70 11 GNAO1,GNAZ,GUCY1A1,GUCY1A2,GUCY1B1,NOS1,PLA2G2D,PLA2G4A,PLA2G4E,PRKCG,RYR1
KEGG_TYPE_II_DIABETES_MELLITUS 4.2e-05 4.8e-04 1813 47 9 ABCC8,CACNA1G,KCNJ11,MAFA,MAPK10,PIK3R5,PRKCZ,SLC2A4,SOCS4
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS 4.4e-05 4.8e-04 1813 96 13 CFL2,HCK,MYO10,PIK3R5,PIP5K1B,PLA2G4A,PLA2G4E,PLPP2,PRKCG,SCIN,VAV1,WAS,WASF3

Num: 10 (Pathways: 18 DK: 14)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (14) CDK19, DSTYK, HIPK3, LRRK1, MAP3K10, MARK4, NEK11, PIP4K2C, PIP5K1C, RPS6KC1, SBK3, SRPK3, STK38L, TTBK2
Light Kinase (32) AAK1, ABR, ACVR1, BRD2, CAMK2D, CSNK1D, DGKD, EIF2AK3, FRK, GSK3B, HK1, ILK, INSR, JAK1, LATS2, MAP2K2, MAP3K8, MAPK1, MAPKAPK2, MST1R, MYLK3, MYLK4, NRBP1, NUAK1, PEAK1, PI4K2A, PINK1, SIK3, TAOK3, TGFBR1, TRPM7, ULK1
Non-kinase Count 1183
label pval fdr signature geneset overlap hits
KEGG_LYSOSOME 0.0e+00 0.0e+00 1229 121 25 ATP6AP1,CD164,CD63,CLN3,CLTCL1,CTNS,CTSA,CTSB,CTSD,CTSF,DNASE2,GAA,GALNS,GNS,IGF2R,LAMP2,MANBA,MCOLN1,NEU1,PLA2G15,PSAP,SCARB2,SLC17A5,SMPD1,TPP1
KEGG_REGULATION_OF_ACTIN_CYTOSKELETON 0.0e+00 0.0e+00 1229 213 28 ACTG1,ARHGEF12,ARHGEF6,ARPC3,BAIAP2,CDC42,CRK,CYFIP1,FGF13,IQGAP1,ITGA1,ITGA7,ITGAV,ITGB1,MAP2K2,MAPK1,MSN,MYL12A,MYL12B,MYL5,MYLK3,PIP4K2C,PIP5K1C,RHOA,RRAS,RRAS2,TIAM2,WASL
KEGG_FOCAL_ADHESION 0.0e+00 0.0e+00 1229 199 25 ACTG1,ARHGAP5,CDC42,COL11A2,COL6A1,COL6A2,CRK,CTNNB1,GSK3B,HGF,ILK,ITGA1,ITGA7,ITGAV,ITGB1,LAMC1,MAPK1,MYL12A,MYL12B,MYL5,MYLK3,PIP5K1C,RAPGEF1,RHOA,THBS3
KEGG_STEROID_BIOSYNTHESIS 0.0e+00 0.0e+00 1229 17 9 CYP51A1,DHCR24,EBP,FDFT1,LSS,MSMO1,NSDHL,SC5D,SOAT1
KEGG_PATHWAYS_IN_CANCER 2.0e-07 6.6e-06 1229 325 26 ARNT,ARNT2,CCDC6,CDC42,CRK,CSF2RA,CTNNA1,CTNNB1,FGF13,FZD8,GSK3B,HGF,ITGAV,ITGB1,JAK1,LAMC1,MAP2K2,MAPK1,NCOA4,PAX8,RALGDS,RHOA,STAT5B,TGFBR1,TRAF6,WNT5B
KEGG_ADHERENS_JUNCTION 2.0e-07 6.6e-06 1229 73 12 ACTG1,BAIAP2,CDC42,CTNNA1,CTNNB1,INSR,IQGAP1,MAPK1,RHOA,SORBS1,TGFBR1,WASL
KEGG_ENDOCYTOSIS 6.0e-07 1.7e-05 1229 181 18 ARAP1,ASAP2,CDC42,CHMP1B,CHMP2A,CLTCL1,CXCR4,DAB2,EPS15,GIT2,MVB12B,PIP5K1C,PSD4,RAB11FIP5,RAB31,RAB5B,SH3GLB1,TRAF6
KEGG_AXON_GUIDANCE 7.0e-07 1.7e-05 1229 129 15 ARHGEF12,CDC42,CHP1,CXCR4,EFNA1,EFNB3,GNAI2,GSK3B,ITGB1,MAPK1,NFAT5,PLXNA3,RHOA,SEMA4B,SEMA6C
KEGG_TERPENOID_BACKBONE_BIOSYNTHESIS 9.0e-07 1.9e-05 1229 15 6 ACAT1,ACAT2,FDPS,HMGCR,HMGCS1,IDI1
KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION 1.1e-06 2.0e-05 1229 116 14 ACTG1,ARHGAP5,CDC42,CTNNA1,CTNNB1,CXCR4,GNAI2,ITGB1,MSN,MYL12A,MYL12B,MYL5,NCF2,RHOA
KEGG_TIGHT_JUNCTION 5.1e-06 8.6e-05 1229 132 14 ACTG1,CDC42,CTNNA1,CTNNB1,EXOC3,EXOC4,GNAI2,MYL12A,MYL12B,MYL5,PATJ,RHOA,RRAS,RRAS2
KEGG_FATTY_ACID_METABOLISM 7.3e-06 1.1e-04 1229 42 8 ACAT1,ACAT2,ACOX1,ACSL1,ADH5,EHHADH,HADHA,HADHB
KEGG_PATHOGENIC_ESCHERICHIA_COLI_INFECTION 8.5e-06 1.2e-04 1229 56 9 ACTG1,ARPC3,CDC42,CTNNB1,ITGB1,LY96,RHOA,WASL,YWHAZ
KEGG_ALZHEIMERS_DISEASE 1.6e-05 2.1e-04 1229 165 15 ADAM17,APP,CAPN1,CHP1,COX6A1,COX6C,EIF2AK3,GRIN2D,GSK3B,ITPR2,LRP1,MAPK1,MT-ATP6,MT-ATP8,PSEN1
KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION 2.8e-05 3.5e-04 1229 115 12 ADCY2,ARHGEF12,CALCRL,CALD1,GNAS,ITPR2,MAP2K2,MAPK1,MYL6,MYL6B,MYLK3,RHOA
KEGG_ECM_RECEPTOR_INTERACTION 4.1e-05 4.8e-04 1229 84 10 COL11A2,COL6A1,COL6A2,ITGA1,ITGA7,ITGAV,ITGB1,LAMC1,SDC2,THBS3
KEGG_TGF_BETA_SIGNALING_PATHWAY 4.6e-05 5.0e-04 1229 85 10 ACVR1,DCN,MAPK1,RHOA,SKP1,SMAD7,SMAD9,TGFBR1,THBS3,ZFYVE16
KEGG_THYROID_CANCER 6.4e-05 6.6e-04 1229 29 6 CCDC6,CTNNB1,MAP2K2,MAPK1,NCOA4,PAX8

Num: 5 (Pathways: 31 DK: 13)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (13) ALPK3, CDC42BPB, CDK15, CDKL5, ICK, NEK10, NEK8, NRBP2, PAK3, PAK6, STK32C, STK36, WNK3
Light Kinase (34) ABL1, AXL, CKB, DGKA, DGKB, DMPK, EIF2AK4, EPHA1, EPHA5, ERBB2, FGR, IGF1R, IKBKB, IKBKE, LIMK2, LRRK2, MAP2K5, MAP3K11, MAP3K12, MAPK3, MYLK, NPR1, PIK3CB, PKDCC, PRKCD, PRKD1, PRKY, RAF1, ROS1, STK16, STRADA, TIE1, TRIO, ULK2
Non-kinase Count 1605
label pval fdr signature geneset overlap hits
KEGG_FOCAL_ADHESION 0.0e+00 0.0e+00 1652 199 37 ACTN1,ACTN4,BAD,BCAR1,CAV3,CCND3,COL1A1,COL1A2,COL3A1,COL5A2,DOCK1,ERBB2,IGF1R,ITGA11,ITGB4,ITGB8,LAMA3,LAMB1,LAMB2,MAPK3,MYL9,MYLK,PAK3,PAK6,PARVB,PDGFC,PDGFD,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PPP1CB,RAC3,RAF1,TLN1,VEGFB,VWF
KEGG_REGULATION_OF_ACTIN_CYTOSKELETON 0.0e+00 0.0e+00 1652 213 30 ACTN1,ACTN4,ARPC5,BCAR1,CFL1,DOCK1,F2R,FGD3,FGF7,ITGA11,ITGB4,ITGB8,LIMK2,MAPK3,MRAS,MYL9,MYLK,PAK3,PAK6,PDGFC,PDGFD,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PIP4K2B,PPP1CB,RAC3,RAF1,SSH3
KEGG_PATHWAYS_IN_CANCER 0.0e+00 0.0e+00 1652 325 36 ABL1,AR,AXIN2,BAD,BMP4,CDKN2B,CTNNA3,ERBB2,FGF7,FZD6,IGF1R,IKBKB,LAMA3,LAMB1,LAMB2,MAPK3,MECOM,MITF,MMP2,PIAS3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PLD1,PPARD,RAC3,RAF1,RXRA,SMAD3,STAT3,STK36,TP53,VEGFB,WNT5A,ZBTB16
KEGG_AXON_GUIDANCE 0.0e+00 1.0e-07 1652 129 21 ABL1,CFL1,CXCL12,EFNA5,EPHA1,EPHA5,GNAI1,LIMK2,MAPK3,NTN4,PAK3,PAK6,PLXNB1,PLXNB2,PLXNB3,PLXNC1,RAC3,SEMA3B,SEMA3C,SEMA3E,SEMA4A
KEGG_PHOSPHATIDYLINOSITOL_SIGNALING_SYSTEM 0.0e+00 1.0e-07 1652 76 16 CALM3,DGKA,DGKB,IMPA2,INPP5A,INPP5D,INPP5J,INPPL1,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PIP4K2B,PLCB1,PLCD4,PLCE1
KEGG_PANCREATIC_CANCER 0.0e+00 2.0e-07 1652 70 15 BAD,ERBB2,IKBKB,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PLD1,RAC3,RAF1,SMAD3,STAT3,TP53,VEGFB
KEGG_FC_GAMMA_R_MEDIATED_PHAGOCYTOSIS 0.0e+00 4.0e-07 1652 96 17 ARPC5,CFL1,DNM1,FCGR2A,INPP5D,LIMK2,MAPK3,MARCKSL1,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PIP4K2B,PLD1,PRKCD,PTPRC,RAF1
KEGG_DRUG_METABOLISM_CYTOCHROME_P450 1.0e-07 2.0e-06 1652 72 14 ALDH3A1,ALDH3B1,CYP2C18,CYP2E1,FMO1,FMO2,FMO3,GSTA1,GSTA2,GSTM2,MAOA,MGST2,UGT1A6,UGT2B11
KEGG_ECM_RECEPTOR_INTERACTION 1.0e-07 2.1e-06 1652 84 15 CD36,COL1A1,COL1A2,COL3A1,COL5A2,DAG1,HSPG2,ITGA11,ITGB4,ITGB8,LAMA3,LAMB1,LAMB2,SV2A,VWF
KEGG_PROSTATE_CANCER 2.0e-07 4.1e-06 1652 89 15 AR,BAD,CREB3L1,ERBB2,IGF1R,IKBKB,MAPK3,PDGFC,PDGFD,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RAF1,TP53
KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION 2.0e-07 4.2e-06 1652 115 17 ACTA2,ACTG2,ADCY6,CALM3,EDNRA,GNAQ,KCNMB3,MAPK3,MRVI1,MYL9,MYLK,NPR1,PLCB1,PPP1CB,PRKCD,RAF1,RAMP1
KEGG_PPAR_SIGNALING_PATHWAY 4.0e-07 5.7e-06 1652 69 13 ACADL,APOC3,AQP7,CD36,CPT2,DBI,OLR1,PLIN1,PPARD,RXRA,SCP2,SLC27A2,SLC27A4
KEGG_MELANOMA 5.0e-07 7.4e-06 1652 71 13 BAD,FGF7,IGF1R,MAPK3,MITF,PDGFC,PDGFD,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RAF1,TP53
KEGG_ENDOMETRIAL_CANCER 9.0e-07 1.1e-05 1652 52 11 AXIN2,BAD,CTNNA3,ERBB2,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RAF1,TP53
KEGG_PHENYLALANINE_METABOLISM 1.0e-06 1.2e-05 1652 18 7 ALDH3A1,ALDH3B1,AOC2,AOC3,HPD,MAOA,NAA80
KEGG_ACUTE_MYELOID_LEUKEMIA 2.3e-06 2.6e-05 1652 57 11 BAD,IKBKB,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PPARD,RAF1,STAT3,ZBTB16
KEGG_CHRONIC_MYELOID_LEUKEMIA 4.6e-06 5.1e-05 1652 73 12 ABL1,BAD,IKBKB,MAPK3,MECOM,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RAF1,SMAD3,TP53
KEGG_COLORECTAL_CANCER 5.4e-06 5.5e-05 1652 62 11 AXIN2,BAD,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RAC3,RAF1,SMAD3,TP53
KEGG_ALDOSTERONE_REGULATED_SODIUM_REABSORPTION 7.6e-06 7.5e-05 1652 42 9 ATP1A2,ATP1A4,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,SCNN1B,SLC9A3R2
KEGG_GAP_JUNCTION 8.2e-06 7.7e-05 1652 90 13 ADCY6,GNAI1,GNAQ,GRM1,HTR2C,MAP2K5,MAPK3,PDGFC,PDGFD,PLCB1,RAF1,TUBA3D,TUBA3E
KEGG_PEROXISOME 9.4e-06 7.8e-05 1652 78 12 ABCD1,DDO,DECR2,ECI2,NUDT12,PEX11A,PEX11B,PEX11G,PEX13,PXMP2,SCP2,SLC27A2
KEGG_INOSITOL_PHOSPHATE_METABOLISM 9.6e-06 7.8e-05 1652 54 10 IMPA2,INPP5A,INPP5J,INPPL1,ISYNA1,PIK3CB,PIP4K2B,PLCB1,PLCD4,PLCE1
KEGG_NON_SMALL_CELL_LUNG_CANCER 9.6e-06 7.8e-05 1652 54 10 BAD,ERBB2,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RAF1,RXRA,TP53
KEGG_RENIN_ANGIOTENSIN_SYSTEM 1.2e-05 9.0e-05 1652 17 6 ACE2,AGT,ANPEP,CPA3,LNPEP,MME
KEGG_CHEMOKINE_SIGNALING_PATHWAY 1.8e-05 1.4e-04 1652 189 19 ADCY6,BCAR1,CCL28,CCR7,CXCL12,CXCR5,FGR,GNAI1,GNG10,IKBKB,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PLCB1,PRKCD,RAF1,STAT3
KEGG_SMALL_CELL_LUNG_CANCER 2.0e-05 1.5e-04 1652 84 12 CDKN2B,IKBKB,LAMA3,LAMB1,LAMB2,PIAS3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RXRA,TP53
KEGG_PROGESTERONE_MEDIATED_OOCYTE_MATURATION 2.3e-05 1.6e-04 1652 85 12 ADCY6,ANAPC11,ANAPC13,GNAI1,IGF1R,MAPK3,PDE3A,PIK3CB,PIK3R1,PIK3R2,PIK3R3,RAF1
KEGG_NEUROTROPHIN_SIGNALING_PATHWAY 7.7e-05 5.1e-04 1652 126 14 ABL1,BAD,BEX3,CALM3,IKBKB,MAP2K5,MAPK3,PIK3CB,PIK3R1,PIK3R2,PIK3R3,PRKCD,RAF1,TP53
KEGG_PURINE_METABOLISM 8.1e-05 5.2e-04 1652 159 16 ADA,ADCY6,AK1,DGUOK,ENTPD4,ENTPD5,NME3,NME4,NPR1,PDE1A,PDE3A,PDE6A,PDE6G,PDE7B,PDE8B,POLR2L
KEGG_COMPLEMENT_AND_COAGULATION_CASCADES 8.7e-05 5.4e-04 1652 69 10 C1R,C3,C4A,C4B,CFB,CR1,F2R,SERPINA5,SERPINF2,VWF
KEGG_METABOLISM_OF_XENOBIOTICS_BY_CYTOCHROME_P450 9.9e-05 5.9e-04 1652 70 10 ALDH3A1,ALDH3B1,CYP2C18,CYP2E1,GSTA1,GSTA2,GSTM2,MGST2,UGT1A6,UGT2B11

Num: 2 (Pathways: 7 DK: 12)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (12) BRSK1, CDK11B, CDK16, CSNK1G3, MAP3K21, MARK3, PHKG1, RIOK1, RIOK2, RPS6KL1, STK40, VRK2
Light Kinase (35) AURKA, CASK, CDK4, CDK8, CSNK1A1, CSNK2A1, DGKG, EIF2AK2, EPHA2, FLT1, GAK, HK2, HUNK, IRAK2, MAP2K1, MAP3K4, MAPK9, MAPKAPK3, MAPKAPK5, MARK2, PAK4, PDPK2P, PIM1, PIM2, PLK2, PLK3, PRKAA1, RPS6KB1, SGK3, TAF1, TBK1, TEX14, TRIB2, TRIB3, TRIM33
Non-kinase Count 1556
label pval fdr signature geneset overlap hits
KEGG_RIBOSOME 0.0e+00 0.0e+00 1603 88 73 FAU,RPL10,RPL10A,RPL11,RPL12,RPL13,RPL13A,RPL14,RPL15,RPL17,RPL18,RPL18A,RPL19,RPL22L1,RPL23,RPL23A,RPL24,RPL26,RPL27,RPL27A,RPL28,RPL29,RPL3,RPL30,RPL31,RPL32,RPL34,RPL35,RPL35A,RPL36,RPL36A,RPL37,RPL37A,RPL38,RPL39,RPL4,RPL5,RPL6,RPL7,RPL8,RPL9,RPLP0,RPLP1,RPLP2,RPS10,RPS11,RPS12,RPS13,RPS15,RPS15A,RPS16,RPS18,RPS19,RPS2,RPS20,RPS21,RPS23,RPS24,RPS25,RPS27,RPS27A,RPS28,RPS29,RPS3,RPS3A,RPS4X,RPS5,RPS6,RPS8,RPS9,RPSA,RSL24D1,UBA52
KEGG_AMINOACYL_TRNA_BIOSYNTHESIS 0.0e+00 0.0e+00 1603 41 16 AARS1,CARS1,DARS1,EARS2,EPRS1,FARSB,GARS1,HARS1,IARS1,KARS1,LARS1,MARS1,PSTK,SARS1,TARS1,YARS1
KEGG_PROTEASOME 0.0e+00 0.0e+00 1603 46 14 PSMA4,PSMA5,PSMA6,PSMB1,PSMB3,PSMC5,PSMD11,PSMD13,PSMD14,PSMD3,PSMD4,PSMD7,PSME4,PSMF1
KEGG_SPLICEOSOME 0.0e+00 0.0e+00 1603 127 21 BUD31,CCDC12,CTNNBL1,CWC15,LSM5,MAGOH,PLRG1,PPIE,PRPF3,SF3A1,SF3B6,SMNDC1,SNRNP27,SNRPB2,SNU13,SRSF1,SRSF3,SRSF7,U2AF1,U2AF2,USP39
KEGG_AMINO_SUGAR_AND_NUCLEOTIDE_SUGAR_METABOLISM 1.0e-06 3.8e-05 1603 44 10 GFPT1,GFPT2,GMPPA,GNPDA1,GNPDA2,HK2,NANS,PGM3,PMM2,UAP1
KEGG_PYRIMIDINE_METABOLISM 1.5e-05 4.8e-04 1603 98 13 CANT1,NME1-NME2,NME2,NT5C,PNP,POLD2,POLE4,POLR1E,POLR2C,POLR2H,POLR2J,POLR3D,PRIM2
KEGG_MAPK_SIGNALING_PATHWAY 2.0e-05 5.3e-04 1603 267 23 CACNA1F,CD14,CRKL,DDIT3,DUSP2,DUSP4,DUSP5,DUSP6,DUSP7,ELK4,FAS,FGF8,GADD45A,MAP2K1,MAP3K4,MAPK9,MAPKAPK3,MAPKAPK5,MAX,MYC,PDGFA,RAC1,RAP1B

Num: 1 (Pathways: 28 DK: 11)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (11) ADCK1, ADCK5, CDC42BPG, COQ8B, CSNK2A3, MAST3, NEK9, PRAG1, PRKACB, STK32A, TAOK2
Light Kinase (31) BCR, BRD3, CKMT1A, CKMT1B, DGKQ, EIF2AK1, EPHA7, EPHB6, ERBB3, ERBB4, KDR, LIMK1, MAP3K13, MAP3K5, MAP4K2, MINK1, PRKACA, PRKCA, PRKCH, PRKX, PTK2B, ROCK2, RPS6KA2, RPS6KA6, SGK1, STK11, STK38, TGFBR2, TNK2, TRIM66, UHMK1
Non-kinase Count 1458
label pval fdr signature geneset overlap hits
KEGG_PEROXISOME 0.0e+00 0.0e+00 1500 78 17 ABCD2,ABCD3,AMACR,CRAT,CROT,FAR2,GSTK1,HMGCL,IDH2,MLYCD,MPV17,PEX1,PEX2,PEX5,PEX7,PMVK,PXMP4
KEGG_ALZHEIMERS_DISEASE 0.0e+00 1.0e-07 1500 165 23 ADAM10,APBB1,ATP5F1C,ATP5F1D,ATP5F1E,ATP5PD,CALM1,CASP9,COX7A2,COX7C,FADD,LPL,MT-CO2,NDUFA4L2,NDUFB1,NDUFB3,NDUFB5,PLCB2,PPP3CB,SNCA,UQCR11,UQCRB,UQCRQ
KEGG_PATHWAYS_IN_CANCER 0.0e+00 1.0e-07 1500 325 33 APPL1,BCL2L1,BCR,CASP9,CDKN1A,COL4A1,COL4A2,FADD,FGF12,FGF5,FN1,FOXO1,FZD1,FZD3,FZD4,GLI2,GLI3,HIF1A,ITGA3,JUP,LAMA1,LAMA5,PRKCA,PTCH1,PTEN,RASSF5,RBX1,RUNX1T1,SLC2A1,STAT1,TGFB1,TGFBR2,WNT11
KEGG_OXIDATIVE_PHOSPHORYLATION 0.0e+00 1.0e-07 1500 131 20 ATP5F1C,ATP5F1D,ATP5F1E,ATP5PD,ATP6V0A1,ATP6V0D1,ATP6V0E2,ATP6V1E2,ATP6V1G2,COX7A2,COX7C,LHPP,MT-CO2,NDUFA4L2,NDUFB1,NDUFB3,NDUFB5,UQCR11,UQCRB,UQCRQ
KEGG_HUNTINGTONS_DISEASE 0.0e+00 1.0e-06 1500 180 22 AP2A2,ATP5F1C,ATP5F1D,ATP5F1E,ATP5PD,CASP9,COX7A2,COX7C,CREB3L2,DLG4,DNAL4,HIP1,MT-CO2,NDUFA4L2,NDUFB1,NDUFB3,NDUFB5,PLCB2,POLR2E,UQCR11,UQCRB,UQCRQ
KEGG_ENDOCYTOSIS 0.0e+00 1.0e-06 1500 181 22 ACAP3,ADRB1,ADRB2,AP2A2,ARRB1,ARRB2,ASAP3,DNAJC6,DNM3,ERBB3,ERBB4,HSPA2,IQSEC1,KDR,LDLRAP1,PARD6A,PSD3,RAB11FIP1,RAB4A,SH3GLB2,TSG101,VPS25
KEGG_PARKINSONS_DISEASE 1.0e-07 1.6e-06 1500 128 18 ATP5F1C,ATP5F1D,ATP5F1E,ATP5PD,CASP9,COX7A2,COX7C,MT-CO2,NDUFA4L2,NDUFB1,NDUFB3,NDUFB5,SEPTIN5,SNCA,UBE2L6,UQCR11,UQCRB,UQCRQ
KEGG_WNT_SIGNALING_PATHWAY 1.0e-07 3.2e-06 1500 150 19 CTNNBIP1,CXXC4,FZD1,FZD3,FZD4,LRP5,PLCB2,PPP2R5A,PPP3CB,PRICKLE1,PRICKLE2,PRKACA,PRKACB,PRKCA,PRKX,RBX1,ROCK2,VANGL1,WNT11
KEGG_VIBRIO_CHOLERAE_INFECTION 5.0e-07 1.0e-05 1500 54 11 ADCY9,ATP6V0A1,ATP6V0D1,ATP6V0E2,ATP6V1E2,ATP6V1G2,MUC2,PRKACA,PRKACB,PRKCA,PRKX
KEGG_MELANOGENESIS 2.0e-06 3.8e-05 1500 101 14 ADCY1,ADCY9,CALM1,CREB3L2,FZD1,FZD3,FZD4,PLCB2,PRKACA,PRKACB,PRKCA,PRKX,TYRP1,WNT11
KEGG_GLYCEROPHOSPHOLIPID_METABOLISM 3.1e-06 5.2e-05 1500 77 12 AGPAT2,CDS1,CHKA,CHKB,DGKQ,ETNK2,GPD1L,LPCAT3,LPCAT4,PLA2G12A,PLA2G2C,TAZ
KEGG_MAPK_SIGNALING_PATHWAY 7.0e-06 9.7e-05 1500 267 23 ARRB1,ARRB2,DUSP14,FGF12,FGF5,GNG12,HSPA2,JUND,MAP3K13,MAP3K5,MAP4K2,PLA2G12A,PLA2G2C,PPP3CB,PRKACA,PRKACB,PRKCA,PRKX,RPS6KA2,RPS6KA6,TAOK2,TGFB1,TGFBR2
KEGG_CALCIUM_SIGNALING_PATHWAY 7.2e-06 9.7e-05 1500 177 18 ADCY1,ADCY9,ADRB1,ADRB2,BDKRB2,CALM1,CHRM3,ERBB3,ERBB4,P2RX1,PLCB2,PLCD3,PPP3CB,PRKACA,PRKACB,PRKCA,PRKX,PTK2B
KEGG_LONG_TERM_POTENTIATION 7.3e-06 9.7e-05 1500 70 11 ADCY1,CALM1,PLCB2,PPP1CA,PPP3CB,PRKACA,PRKACB,PRKCA,PRKX,RPS6KA2,RPS6KA6
KEGG_AXON_GUIDANCE 8.2e-06 1.0e-04 1500 129 15 ABLIM1,ABLIM2,EFNB2,EPHA7,EPHB6,LIMK1,PPP3CB,ROBO2,ROCK2,SEMA3F,SEMA4F,SEMA4G,SEMA5A,SEMA6D,SRGAP1
KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_HEPARAN_SULFATE 8.6e-06 1.0e-04 1500 26 7 B3GALT6,B3GAT3,GLCE,HS3ST1,NDST2,NDST3,XYLT2
KEGG_LEUKOCYTE_TRANSENDOTHELIAL_MIGRATION 1.1e-05 1.2e-04 1500 116 14 ARHGAP35,CLDN11,CLDN16,CLDN9,CYBA,EZR,PECAM1,PRKCA,PTK2B,RAPGEF4,RASSF5,ROCK2,VAV3,VCL
KEGG_SYSTEMIC_LUPUS_ERYTHEMATOSUS 2.0e-05 2.1e-04 1500 139 15 H2AC11,H2AC19,H2AC6,H2AC8,H2AJ,H2AW,H2BC21,H2BC4,H2BC5,H2BC6,H3C10,H3C12,H4C14,H4C9,HLA-DMA
KEGG_O_GLYCAN_BIOSYNTHESIS 2.4e-05 2.3e-04 1500 30 7 C1GALT1C1,GALNT1,GALNT11,GALNT18,GALNT2,GALNT4,GALNT7
KEGG_SULFUR_METABOLISM 2.5e-05 2.3e-04 1500 13 5 BPNT1,CHST12,PAPSS1,SULT1A4,SUOX
KEGG_REGULATION_OF_ACTIN_CYTOSKELETON 2.6e-05 2.3e-04 1500 213 19 ARHGAP35,ARHGEF4,BDKRB2,CHRM3,EZR,FGF12,FGF5,FN1,GNG12,IQGAP2,ITGA3,LIMK1,MYH10,PPP1CA,ROCK2,SSH2,TIAM1,VAV3,VCL
KEGG_OOCYTE_MEIOSIS 3.3e-05 2.8e-04 1500 112 13 ADCY1,ADCY9,CALM1,PPP1CA,PPP2R5A,PPP3CB,PRKACA,PRKACB,PRKX,RBX1,RPS6KA2,RPS6KA6,YWHAH
KEGG_GLYCOSAMINOGLYCAN_BIOSYNTHESIS_CHONDROITIN_SULFATE 3.6e-05 2.9e-04 1500 22 6 B3GALT6,B3GAT3,CHST12,CHST7,CHSY3,XYLT2
KEGG_VASCULAR_SMOOTH_MUSCLE_CONTRACTION 4.3e-05 3.4e-04 1500 115 13 ADCY1,ADCY9,CALM1,PLA2G12A,PLA2G2C,PLCB2,PPP1CA,PRKACA,PRKACB,PRKCA,PRKCH,PRKX,ROCK2
KEGG_CHEMOKINE_SIGNALING_PATHWAY 6.2e-05 4.6e-04 1500 189 17 ADCY1,ADCY9,ARRB1,ARRB2,CCR10,GNB5,GNG12,PLCB2,PRKACA,PRKACB,PRKX,PTK2B,ROCK2,SHC2,STAT1,TIAM1,VAV3
KEGG_INSULIN_SIGNALING_PATHWAY 6.9e-05 4.9e-04 1500 137 14 CALM1,FOXO1,G6PC,IRS1,LIPE,PDE3B,PPP1CA,PPP1R3D,PRKACA,PRKACB,PRKX,PYGB,SHC2,SREBF1
KEGG_GAP_JUNCTION 8.1e-05 5.6e-04 1500 90 11 ADCY1,ADCY9,ADRB1,GJA1,LPAR1,PLCB2,PRKACA,PRKACB,PRKCA,PRKX,TUBB3
KEGG_GLYCEROLIPID_METABOLISM 9.7e-05 6.5e-04 1500 49 8 AGPAT2,ALDH3A2,ALDH7A1,DGAT1,DGAT2,DGKQ,LPL,TKFC

Num: 9 (Pathways: 3 DK: 9)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (9) ALPK2, BRSK2, CDK18, CDKL2, LTK, MAP3K14, PXK, STK31, STK33
Light Kinase (19) ACVR1B, AKT3, BRDT, DAPK3, EPHA4, ERN1, FES, FYN, GRK5, LCK, MAK, MAP3K9, MAP4K5, MERTK, NPR2, PRKCE, PRKG1, TNK1, TNNI3K
Non-kinase Count 962
label pval fdr signature geneset overlap hits
KEGG_OXIDATIVE_PHOSPHORYLATION 4.0e-07 0.00006 990 131 14 ATP4B,ATP6V1F,COX8C,MT-CO1,MT-CO3,MT-CYB,MT-ND1,MT-ND3,MT-ND4,MT-ND4L,NDUFA1,NDUFA4,NDUFB4,NDUFB9
KEGG_NEUROACTIVE_LIGAND_RECEPTOR_INTERACTION 6.0e-07 0.00006 990 272 20 ADRA1B,C5AR1,GABBR2,GABRR2,GIPR,GRIA2,GRIK2,GRIN2A,MAS1,OPRM1,OXTR,P2RY2,P2RY4,PLG,PRLHR,PRSS3,PTGIR,PTH2R,TBXA2R,THRB
KEGG_PARKINSONS_DISEASE 1.7e-06 0.00011 990 128 13 COX8C,MT-CO1,MT-CO3,MT-CYB,MT-ND1,MT-ND3,MT-ND4,MT-ND4L,NDUFA1,NDUFA4,NDUFB4,NDUFB9,UBE2J2

Num: 3 (Pathways: 5 DK: 8)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (8) ADCK2, CAMKK2, CDK13, CSNK1G2, MAST4, NEK6, SCYL3, TP53RK
Light Kinase (16) ALPK1, CLK2, EGFR, MTOR, NLK, PDGFRA, PDK4, PIK3CG, PKN1, PKN2, ROR1, RYK, STK24, STK39, TBRG4, TEK
Non-kinase Count 876
label pval fdr signature geneset overlap hits
KEGG_OXIDATIVE_PHOSPHORYLATION 0.0e+00 3.1e-06 900 131 15 ATP5F1A,ATP5MC1,ATP5MC2,ATP5ME,ATP5PO,COX17,COX8A,NDUFA7,NDUFB6,NDUFS1,NDUFV1,NDUFV3,PPA1,PPA2,UQCRFS1
KEGG_HUNTINGTONS_DISEASE 2.0e-07 1.8e-05 900 180 16 ATP5F1A,ATP5MC1,ATP5MC2,ATP5PO,BDNF,COX8A,CREB3L4,IFT57,NDUFA7,NDUFB6,NDUFS1,NDUFV1,NDUFV3,POLR2G,POLR2I,UQCRFS1
KEGG_SELENOAMINO_ACID_METABOLISM 3.0e-07 1.8e-05 900 26 7 AHCY,CBS,GGT5,LCMT2,METTL6,SCLY,SEPHS2
KEGG_PARKINSONS_DISEASE 3.8e-06 1.8e-04 900 128 12 ATP5F1A,ATP5MC1,ATP5MC2,ATP5PO,COX8A,NDUFA7,NDUFB6,NDUFS1,NDUFV1,NDUFV3,PARK7,UQCRFS1
KEGG_N_GLYCAN_BIOSYNTHESIS 1.7e-05 6.5e-04 900 46 7 ALG2,ALG3,B4GALT2,DPAGT1,MGAT1,MGAT2,RFT1

Num: 13 (Pathways: 7 DK: 6)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (6) CDK20, CLK4, DYRK3, DYRK4, NEK3, NUAK2
Light Kinase (12) ACVR2B, AURKC, BMPR1B, BRAF, CDK7, CSNK1E, MAP3K20, PIM3, PTK6, RIPK2, TRIB1, TRPM6
Non-kinase Count 536
label pval fdr signature geneset overlap hits
KEGG_PATHWAYS_IN_CANCER 0.0e+00 0.0e+00 554 325 22 BIRC2,BMP2,BRAF,CDKN1B,CSF3R,DVL1,ETS1,FGF2,IKBKG,IL6,ITGA2B,LAMB3,LAMC2,MMP1,NFKB2,NFKBIA,PPARG,PTGS2,SMAD2,STAT5A,TRAF1,VEGFA
KEGG_NOD_LIKE_RECEPTOR_SIGNALING_PATHWAY 0.0e+00 2.0e-07 554 62 10 BIRC2,CXCL1,IKBKG,IL1B,IL6,NFKBIA,NLRC4,NLRP3,RIPK2,TNFAIP3
KEGG_CYTOKINE_CYTOKINE_RECEPTOR_INTERACTION 0.0e+00 6.0e-07 554 265 17 ACVR2B,BMP2,BMPR1B,CSF2,CSF3,CSF3R,CXCL1,CXCL10,IL1A,IL1B,IL6,INHBA,LTBR,PRLR,TNFRSF12A,TSLP,VEGFA
KEGG_CIRCADIAN_RHYTHM_MAMMAL 2.0e-07 9.1e-06 554 13 5 BHLHE40,BHLHE41,CSNK1E,NPAS2,PER1
KEGG_SMALL_CELL_LUNG_CANCER 4.0e-07 1.5e-05 554 84 9 BIRC2,CDKN1B,IKBKG,ITGA2B,LAMB3,LAMC2,NFKBIA,PTGS2,TRAF1
KEGG_MAPK_SIGNALING_PATHWAY 1.1e-05 3.3e-04 554 267 13 BRAF,DUSP10,DUSP16,DUSP8,FGF2,GADD45B,IKBKG,IL1A,IL1B,MAP3K20,NFKB2,NGF,RELB
KEGG_RIG_I_LIKE_RECEPTOR_SIGNALING_PATHWAY 1.4e-05 3.8e-04 554 71 7 CXCL10,DDX58,DHX58,IFIH1,IKBKG,ISG15,NFKBIA

Num: 6 (Pathways: 3 DK: 5)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (5) CDK14, OBSCN, STK17A, STK17B, TSSK4
Light Kinase (17) AATK, BLVRA, GRK3, GRK4, MAP3K1, MAPK13, MET, MYO3B, NTRK3, OXSR1, PDK3, PIK3CD, PRKCI, RIPK4, SNRK, SYK, TNIK
Non-kinase Count 550
label pval fdr signature geneset overlap hits
KEGG_ENDOCYTOSIS 0.0e+00 6.0e-07 572 181 15 ACAP1,ARFGAP1,CBLB,CHMP2B,CHMP4C,EHD4,GRK3,GRK4,HLA-B,LDLR,MET,PIKFYVE,PRKCI,SH3GL3,VPS37B
KEGG_NEUROTROPHIN_SIGNALING_PATHWAY 2.1e-06 1.9e-04 572 126 10 ARHGDIB,IRS2,MAGED1,MAP3K1,MAPK13,NTRK3,PIK3CD,PLCG2,SH2B2,SHC3
KEGG_FOCAL_ADHESION 3.7e-06 2.3e-04 572 199 12 CCND2,ITGA2,ITGB3,ITGB5,MET,PDGFB,PIK3CD,SHC3,SPP1,VASP,VEGFC,VTN

Num: 15 (Pathways: 5 DK: 5)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (5) CDC42BPA, CDK10, POMK, PSKH1, TSSK6
Light Kinase (16) CAMK1, CDK6, CHEK2, DCLK2, FASTK, LATS1, MAPK12, MAPK14, MOK, PIK3R4, PRKG2, RPS6KA4, RPS6KB2, STK25, TYK2, WNK4
Non-kinase Count 575
label pval fdr signature geneset overlap hits
KEGG_OXIDATIVE_PHOSPHORYLATION 0.0e+00 0.0e+00 596 131 15 ATP5MC3,ATP5MF,COX15,COX7B,NDUFA2,NDUFA3,NDUFB10,NDUFB2,NDUFB7,NDUFC1,NDUFS2,NDUFS5,NDUFS6,SDHA,UQCR10
KEGG_ALZHEIMERS_DISEASE 0.0e+00 0.0e+00 596 165 16 ATP5MC3,CASP8,COX7B,NDUFA2,NDUFA3,NDUFB10,NDUFB2,NDUFB7,NDUFC1,NDUFS2,NDUFS5,NDUFS6,PPP3CA,SDHA,TNFRSF1A,UQCR10
KEGG_HUNTINGTONS_DISEASE 0.0e+00 0.0e+00 596 180 16 ATP5MC3,BAX,CASP8,COX7B,NDUFA2,NDUFA3,NDUFB10,NDUFB2,NDUFB7,NDUFC1,NDUFS2,NDUFS5,NDUFS6,SDHA,SP1,UQCR10
KEGG_PARKINSONS_DISEASE 0.0e+00 2.0e-07 596 128 13 ATP5MC3,COX7B,NDUFA2,NDUFA3,NDUFB10,NDUFB2,NDUFB7,NDUFC1,NDUFS2,NDUFS5,NDUFS6,SDHA,UQCR10
KEGG_P53_SIGNALING_PATHWAY 1.7e-05 6.3e-04 596 68 7 BAX,CASP8,CCNB3,CDK6,CHEK2,RPRM,SHISA5

Num: 8 (Pathways: 13 DK: 4)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (4) EEF2K, PKMYT1, PRPF4B, RSKR
Light Kinase (23) AKT1, ATR, BUB1B, CDC7, CHUK, CIT, EPHA3, FASTKD1, FASTKD2, FASTKD3, FASTKD5, GRK6, HASPIN, MAP3K7, PBK, PI4K2B, PLK1, PRKDC, RPS6KA1, STRADB, TRIM28, TTK, VRK1
Non-kinase Count 1112
label pval fdr signature geneset overlap hits
KEGG_PYRIMIDINE_METABOLISM 0.0e+00 0.0e+00 1139 98 29 CAD,DHODH,DTYMK,DUT,ENTPD6,NME1,PNPT1,POLA1,POLA2,POLD1,POLE2,POLE3,POLR1A,POLR1B,POLR1C,POLR2B,POLR2D,POLR2F,POLR2J3,POLR2K,POLR3B,POLR3G,POLR3H,POLR3K,PRIM1,RRM2,TK1,TYMS,UMPS
KEGG_DNA_REPLICATION 0.0e+00 0.0e+00 1139 36 20 DNA2,FEN1,LIG1,MCM2,MCM5,MCM6,POLA1,POLA2,POLD1,POLE2,POLE3,PRIM1,RFC2,RFC3,RFC4,RFC5,RNASEH1,RPA1,RPA3,SSBP1
KEGG_PURINE_METABOLISM 0.0e+00 0.0e+00 1139 159 34 ADCY3,ENTPD2,ENTPD6,GART,HPRT1,IMPDH1,NME1,NUDT5,PAICS,PDE4A,PDE7A,PNPT1,POLA1,POLA2,POLD1,POLE2,POLE3,POLR1A,POLR1B,POLR1C,POLR2B,POLR2D,POLR2F,POLR2J3,POLR2K,POLR3B,POLR3G,POLR3H,POLR3K,PPAT,PRIM1,PRPS1,PRPS2,RRM2
KEGG_CELL_CYCLE 0.0e+00 0.0e+00 1139 124 29 ANAPC1,ANAPC10,ANAPC4,ATR,BUB1B,BUB3,CCNE1,CDC20,CDC45,CDC7,DBF4,E2F4,HDAC2,MAD2L1,MCM2,MCM5,MCM6,ORC1,ORC2,ORC5,PKMYT1,PLK1,PRKDC,PTTG1,SKP2,SMC1A,TFDP1,TGFB2,TTK
KEGG_SPLICEOSOME 0.0e+00 0.0e+00 1139 127 28 AQR,CDC5L,DHX15,EFTUD2,HNRNPC,LSM3,LSM6,LSM7,NCBP1,PPIH,PPIL1,PRPF19,PRPF38B,PRPF4,PRPF40A,SF3B4,SNRNP200,SNRNP40,SNRNP70,SNRPC,SNRPD1,SNRPD3,SNRPF,SNRPG,SRSF10,SRSF9,THOC3,TXNL4A
KEGG_MISMATCH_REPAIR 0.0e+00 0.0e+00 1139 23 13 EXO1,LIG1,MLH1,MLH3,MSH6,POLD1,RFC2,RFC3,RFC4,RFC5,RPA1,RPA3,SSBP1
KEGG_HOMOLOGOUS_RECOMBINATION 0.0e+00 0.0e+00 1139 28 12 BLM,EME1,MRE11,POLD1,RAD51C,RAD54B,RPA1,RPA3,SSBP1,TOP3B,XRCC2,XRCC3
KEGG_RNA_POLYMERASE 0.0e+00 0.0e+00 1139 29 12 POLR1A,POLR1B,POLR1C,POLR2B,POLR2D,POLR2F,POLR2J3,POLR2K,POLR3B,POLR3G,POLR3H,POLR3K
KEGG_BASE_EXCISION_REPAIR 0.0e+00 0.0e+00 1139 35 12 APEX1,APEX2,FEN1,HMGB1,LIG1,NEIL2,NTHL1,PARP1,POLD1,POLE2,POLE3,TDG
KEGG_NUCLEOTIDE_EXCISION_REPAIR 0.0e+00 1.0e-07 1139 44 11 GTF2H3,LIG1,POLD1,POLE2,POLE3,RFC2,RFC3,RFC4,RFC5,RPA1,RPA3
KEGG_UBIQUITIN_MEDIATED_PROTEOLYSIS 0.0e+00 2.0e-07 1139 134 17 ANAPC1,ANAPC10,ANAPC4,BRCA1,CDC20,CUL2,FANCL,PRPF19,SAE1,SKP2,UBE2G2,UBE2L3,UBE2N,UBE2NL,UBE2S,UBE3C,VHL
KEGG_OOCYTE_MEIOSIS 0.0e+00 6.0e-07 1139 112 15 ADCY3,ANAPC1,ANAPC10,ANAPC4,CCNE1,CDC20,FBXO5,MAD2L1,PKMYT1,PLK1,PPP1CC,PTTG1,RPS6KA1,SGO1,SMC1A
KEGG_AMINOACYL_TRNA_BIOSYNTHESIS 3.6e-05 5.1e-04 1139 41 7 AARS2,DARS2,LARS2,MARS2,NARS2,RARS1,SARS2

Num: 12 (Pathways: 14 DK: 4)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (4) BCKDK, PKN3, TBCK, TSSK3
Light Kinase (15) AKT2, BMPR1A, DDR1, DGKH, DGKI, HIPK2, IRAK1, MAP3K3, MAP4K3, PDPK1, PIK3CA, RIPK1, SIK2, TRRAP, WNK1
Non-kinase Count 394
label pval fdr signature geneset overlap hits
KEGG_ENDOMETRIAL_CANCER 2.0e-07 2.0e-05 413 52 7 AKT2,HRAS,NRAS,PDPK1,PIK3CA,SOS1,SOS2
KEGG_FC_EPSILON_RI_SIGNALING_PATHWAY 3.0e-07 2.0e-05 413 79 8 AKT2,HRAS,NRAS,PDPK1,PIK3CA,PLA2G4B,SOS1,SOS2
KEGG_NON_SMALL_CELL_LUNG_CANCER 3.0e-07 2.0e-05 413 54 7 AKT2,HRAS,NRAS,PDPK1,PIK3CA,SOS1,SOS2
KEGG_PROSTATE_CANCER 8.0e-07 3.7e-05 413 89 8 AKT2,EP300,HRAS,NRAS,PDPK1,PIK3CA,SOS1,SOS2
KEGG_NEUROTROPHIN_SIGNALING_PATHWAY 1.2e-06 4.3e-05 413 126 9 AKT2,HRAS,IRAK1,MAP3K3,NRAS,PDPK1,PIK3CA,SOS1,SOS2
KEGG_RENAL_CELL_CARCINOMA 1.9e-06 5.9e-05 413 70 7 AKT2,EP300,HRAS,NRAS,PIK3CA,SOS1,SOS2
KEGG_INSULIN_SIGNALING_PATHWAY 2.3e-06 6.2e-05 413 137 9 AKT2,HRAS,NRAS,PDPK1,PHKB,PIK3CA,PRKAR1A,SOS1,SOS2
KEGG_ACUTE_MYELOID_LEUKEMIA 7.8e-06 1.8e-04 413 57 6 AKT2,HRAS,NRAS,PIK3CA,SOS1,SOS2
KEGG_GLIOMA 1.7e-05 3.5e-04 413 65 6 AKT2,HRAS,NRAS,PIK3CA,SOS1,SOS2
KEGG_GNRH_SIGNALING_PATHWAY 2.2e-05 4.1e-04 413 101 7 HRAS,MAP3K3,MMP14,NRAS,PLA2G4B,SOS1,SOS2
KEGG_CHRONIC_MYELOID_LEUKEMIA 3.3e-05 5.3e-04 413 73 6 AKT2,HRAS,NRAS,PIK3CA,SOS1,SOS2
KEGG_T_CELL_RECEPTOR_SIGNALING_PATHWAY 3.4e-05 5.3e-04 413 108 7 AKT2,HRAS,NRAS,PDPK1,PIK3CA,SOS1,SOS2
KEGG_B_CELL_RECEPTOR_SIGNALING_PATHWAY 3.8e-05 5.5e-04 413 75 6 AKT2,HRAS,NRAS,PIK3CA,SOS1,SOS2
KEGG_FOCAL_ADHESION 4.6e-05 6.2e-04 413 199 9 AKT2,HRAS,ITGA10,PARVA,PDPK1,PIK3CA,SOS1,SOS2,ZYX

Num: 7 (Pathways: 3 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) MKNK2, NIM1K
Light Kinase (5) DYRK1A, MAP3K2, PDK1, PRKAA2, TEC
Non-kinase Count 390
label pval fdr signature geneset overlap hits
KEGG_GLYCOLYSIS_GLUCONEOGENESIS 0.0e+00 3.0e-07 397 62 9 ALDOA,ENO1,ENO2,GAPDH,GPI,LDHA,PGK1,PKM,TPI1
KEGG_PENTOSE_PHOSPHATE_PATHWAY 2.2e-06 2.0e-04 397 27 5 ALDOA,GPI,PGD,TALDO1,TKT
KEGG_FRUCTOSE_AND_MANNOSE_METABOLISM 7.1e-06 4.4e-04 397 34 5 AKR1B1,AKR1B10,ALDOA,PFKFB4,TPI1

Num: 14 (Pathways: 0 DK: 2)

The blue dots indicate the mean fold change, while the red dots indicate the overall means. The boxplots show the distribution of all the genes in the cluster. The kinases are highlighted with the lines.

gene_type info
Dark Kinase (2) PI4KA, RNASEL
Light Kinase (16) BMPR2, CDK5, EPHA10, EPHB4, FPGT-TNNI3K, JAK3, MAP2K4, PDGFRB, PDK2, PIK3C2A, PRKD3, PTK7, ROCK1, SPEG, SRC, TRIM24
Non-kinase Count 435
label pval fdr signature geneset overlap hits